Batch effect in whole genome data
I am working with Complete genomics (WGS) data from assembled with pipeline version 2.5. I need to analyze 1000 genome data along with the VCF files for the samples I have. Since the 1K genome project data are from 2.0.0 version, I was wondering if this is something I should be concerned about. If there are any other batch effects, what would you normally correct for while working with different version of complete genomics data?
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